PacBio/Illumina gap patching in ALLPATHS-LG now faster

As of revision 37655, the algorithm that computes the consensus of PacBio reads that patch a gap between ‘Illumina’ contigs is now ~100 times faster. For bacterial genomes it was taking several hours. The speedup was obtained by replacing an iterative Smith-Waterman algorithm by an algorithm that produces an initial alignment then refines it iteratively.